One recurring challenge in molecular modeling is adapting tools to workflows that evolve quickly. Whether you’re connecting to external software, automating repetitive tasks, or introducing new computational methods, it’s often difficult to find a flexible and integrated platform.
This is where SAMSON apps come in.
In SAMSON, an app can represent virtually any type of molecular modeling functionality. Whether you’re docking ligands using established tools like AutoDock Vina, querying remote services for calculations, or wrapping your own code into a tool others can use—apps are the way to get it done within the same molecular design environment.
So what are these SAMSON apps, really?
Apps as Modular Functionality
An app in SAMSON is a self-contained extension that you can install to add new capabilities to the software. These can be as simple as utilities (for example, exporting data) or as complex as sophisticated simulations or AI-powered analysis. The advantage is that you can access all this functionality directly within the SAMSON platform, where your models already live.
This solves common pain points:
- No more jumping between programs and losing context
- Easier reproducibility, since your workflow lives in the same environment
- Opportunity to build on community-made tools designed for the same infrastructure
Where to Find and Add Apps
By default, SAMSON comes with a core set of apps already installed. These include visualization tools, structure builders, and basic analysis functions. But you can also add more apps at any time from SAMSON Connect, a curated repository of extensions created by the scientific community.
Navigating to Home > Apps in SAMSON will show you the apps currently available in your environment. From there, you can launch, manage, or uninstall them as needed.
What’s Under the Hood?
Apps can be built using the SAMSON Application Programming Interface (API), which allows developers to tap into all aspects of the platform—from geometry and simulation tools to UI components and data management. If you’re familiar with C++ and want full control, this is your path. But if you’re new to development, SAMSON also offers tools like the Extension Generator to help you get started without diving deep into the code immediately.
In fact, developing your own app could mean simply wrapping a set of commands you use frequently and exposing them via a convenient user interface in SAMSON. That means your personal workflow becomes repeatable—not just by you, but by collaborators too.
Above is an example of the AutoDock Vina Extended App, which integrates the popular ligand docking software into SAMSON, showing how tightly third-party tools can be woven into the modeling interface.
Want to Try?
If you’re already using SAMSON and haven’t checked out its apps, it’s worth exploring how they can make your modeling work easier. And if you’re developing your own tools, knowing that others can use them from within a shared modeling environment is a big plus for dissemination.
You can check out the full list of apps and learn how to develop your own at the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.